DNA confirms elusive Night Parrot found
By Birding-Aus, on August 10th, 2013
DNA – Most specimens (?all but 3 perhaps) collected before 1900, so not sure how useful it would be. I’m ignorant of molecular approaches, but this detailed type of analysis may not be possible on gnarly old specimens (?better on blood and fresh tissue? – of which there is none) >>>>>>>>>>>> To: birding-aus@lists.vicnet.net.au Subject: DNA confirms elusive Night Parrot found From: Andrew Hobbs <pardalote@iinet.net.au> Date: Sat, 10 Aug 2013 14:22:41 +0800 There are apparently 22 known specimens in various museums around the world. I would think it quite possible to use DNA analysis on those to make some estimates of population sizes etc. and their relationship to the recent samples. I would be surprised if that is not already being done or at least considered. Cheers Andrew =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) to: birding-aus-request@vicnet.net.au http://birding-aus.org ===============================
The way population is estimated is essentially just comparing how much genetic diversity there is between species. Low genetic diversity implies a small population, while high genetic diversity implies a bigger population. There are a number of biological assumptions required for this to work though. In particular it assumes that that population trends have been consistent in recent years, and that the species is a “K” species (has few offspring and relatively stable populations, rather than many offspring and a boom and bust cycle). If you can get a good estimate of the rate of genetic change over time (and we do have that), and you have a good estimate of the amount of genetic diversity between some individuals, you can use statistical methods to create a predictive model of the size the population (which will take into account the possibility of by chance only taking samples from closely related birds within a much larger population). There’s certainly uncertainty, but unless Night Parrots have a significantly different mating behaviour to their nearest relatives, or the population has changed very significantly very recently, an estimate should within an order of magnitude. You don’t need to individually map the entire genome to determine genetic diversity. The easiest technique is to extract DNA and replicate it, and then cut it up into smaller bits and check the differences in the ratios of the weights of each small sections of DNA. This is what the “lines” you see on DNA test on TV are – just cut up segments of DNA that have been placed on an electrolysed agar sheet and have along the sheet at different speeds depending on their weight. Of course there are much more sophisticated techniques which give you a better picture too. I’d have to go back to the text books to remember which would be best here 😛 Jeremy On 12 August 2013 11:57, colin trainor < halmahera@hotmail.com> wrote: =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Hi Peter, I don’t understand either, but it is not a simple analysis like determining sex, or whether one species is different to another. The key element is good quality tissue to begin with. I think that means that contemporary samples are needed, and that would also include the molecular “footprint” of the species undoubted decline [if there is one showing in the molecules, we can assume that this is likely] since roughly 1890 (perhaps before). I’m familiar with one molecular study that compared Australian Zebra Finch [Genome known!], with Lesser Sundas Zebra Finch (usually still considered one species, which is fair). They compared about 30 Aust birds (sample specimens) from several sites, with 12 birds from Lombok and Timor – Indonesia [tissue specimens well preserved]. The study estimated that 9 individual Zebra finches colonised the Lesser Sundas from Australia, that that occurred at an estimated 1.9 million yrs before present (95% interval: 1.2-2.8 million years); and that the current Lesser Sunda population is around 18000-26000 birds; and the Australian population at 1.3 million and 7 million (using different analyses). These are only estimates [not necessarily “reality”], based on the analysis with the many assumptions and limitations discussed. I guess it does highlight the difficulties/complexities of such a study, even with the best (or second best) known bird species on the planet. Colin =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Thanks for all that, Colin. I don’t understand how DNA analysis gives a population estimate. Is it to do with the number of ancestors each bird must have had in order to have that amount of variation in its DNA? And if you could get the necessary samples, would you know when that population estimate was valid for? I assume the estimate derived from, say, 20 samples collected 100 years ago would be no different to 20 collected today, yet the population is likely different today to 100 years ago. Even 100 years ago there might have been a tiny fraction of the population 200 years ago. Peter Shute =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Clive, if funding for threatened species was given for the least numerous, Orange-bellied Parrot funding would flow like rivers in flood. Alas, it’s inconsistent and tenuous; eg a recent application for a Commonwealth Caring for our Country grant for winter survey coordination was unsuccessful. My guess is that funding is currently attached to species with good chances of recovery. At fewer than 50 in the wild, the OBP has pretty poor chances of that, yet, incredibly, it continues to defy the odds. Long may it do so. =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Colin, it’s actually very feasible, in fact highly important DNA has been extracted from early human fossils that are 100s or thousands of years old, that has been used to build a picture of human evolution. DNA extracted from frozen mammoth carcases in Siberia have led to some researchers to propose reviving mammoth as a species (I truly hope this does not happen, but that’s not a discussion for here.) The same has been proposed for thylacines using DNA extracted from preserved joeys in museums. In other words recovery of DNA from museum specimens is well-established science. It doesn’t need to be a complete genome, just enough long fragments to distinguish night parrot from its closest relatives (presumably ground parrot and western ground parrot.) Also distinguishing between human and parrot DNA would be a very simple exercise – much more so than for ancient humans as described above. Basically the scientists can look at a series of bands on a screen and see which ones are human and which non-human, almost as easily as they could distinguish a human and a bird footprint. —–Original Message—– Sent: Saturday, August 10, 2013 7:15 PM DNA – Most specimens (?all but 3 perhaps) collected before 1900, so not sure how useful it would be. I’m ignorant of molecular approaches, but this detailed type of analysis may not be possible on gnarly old specimens (?better on blood and fresh tissue? – of which there is none) birding-aus@lists.vicnet.net.au DNA confirms elusive Night Parrot found Andrew Hobbs < pardalote@iinet.net.au> Sat, 10 Aug 2013 14:22:41 +0800 There are apparently 22 known specimens in various museums around the world. I would think it quite possible to use DNA analysis on those to make some estimates of population sizes etc. and their relationship to the recent samples. I would be surprised if that is not already being done or at least considered. Cheers Andrew =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org =============================== =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Thanks for posting the link, David. John Young sent me a copy of the WA Museum press release yesterday, with permission to post it on the Birding-Aus website. I think it is the same wording from the page you linked to. Anyway, it’s here as a downloadable PDF for anyone who wants a copy: http://birding-aus.org/?page_id=9 Kind regards Russell Woodford On 9 August 2013 18:53, David Clark < meathead.clark5@gmail.com> wrote: =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================
Interesting discussion! I always wondered how the population of a cryptic, nocturnal species could be estimated when virtually nothing is known of its behaviour, range, etc. I recently attended a presentation on the ‘de-extinction’ of the Thylacine and Gastric-brooding Frog and I was surprised to learn that the DNA extracted from a preserved Thylacine pup was largely human. Successive curators couldn’t resist the temptation to handle the specimen. I would imagine that the Night Parrot specimens have been fondled too. Cheers David On Sat, Aug 10, 2013 at 7:15 PM, colin trainor < halmahera@hotmail.com>wrote: =============================== To unsubscribe from this mailing list, send the message: unsubscribe (in the body of the message, with no Subject line) http://birding-aus.org ===============================